#setwd('/afs/inf.ed.ac.uk/user/s17/s1725186/Documents/PhD-Models/FirstPUModel/RMarkdowns')
library(tidyverse) ; library(reshape2) ; library(glue) ; library(plotly) ; library(dendextend)
library(RColorBrewer) ; library(viridis) ; require(gridExtra) ; library(GGally)
library(knitr)
library(biomaRt)
library(clusterProfiler) ; library(ReactomePA) ; library(DOSE)
Load preprocessed dataset (preprocessing code in 19_10_14_data_preprocessing.Rmd) and clustering (pipeline in 19_10_21_WGCNA.Rmd)
# Gandal dataset
load('./../Data/preprocessed_data.RData')
datExpr = datExpr %>% data.frame
DE_info = DE_info %>% data.frame
# GO Neuronal annotations: regex 'neuron' in GO functional annotations and label the genes that make a match as neuronal
GO_annotations = read.csv('./../Data/genes_GO_annotations.csv')
GO_neuronal = GO_annotations %>% filter(grepl('neuron', go_term)) %>%
mutate('ID'=as.character(ensembl_gene_id)) %>%
dplyr::select(-ensembl_gene_id) %>% distinct(ID) %>%
mutate('Neuronal'=1)
# SFARI Genes
SFARI_genes = read_csv('./../../../SFARI/Data/SFARI_genes_01-03-2020_w_ensembl_IDs.csv')
SFARI_genes = SFARI_genes[!duplicated(SFARI_genes$ID) & !is.na(SFARI_genes$ID),]
# Clusterings
clusterings = read_csv('./../Data/clusters.csv')
# Update DE_info with SFARI and Neuronal information
genes_info = DE_info %>% mutate('ID'=rownames(.)) %>% left_join(SFARI_genes, by='ID') %>%
mutate(`gene-score`=ifelse(is.na(`gene-score`), 'None', `gene-score`)) %>%
left_join(GO_neuronal, by='ID') %>% left_join(clusterings, by='ID') %>%
mutate(Neuronal=ifelse(is.na(Neuronal), 0, Neuronal)) %>%
mutate(gene.score=ifelse(`gene-score`=='None' & Neuronal==1, 'Neuronal', `gene-score`),
significant=padj<0.05 & !is.na(padj))
clustering_selected = 'DynamicHybrid'
genes_info$Module = genes_info[,clustering_selected]
dataset = read.csv(paste0('./../Data/dataset_', clustering_selected, '.csv'))
dataset$Module = dataset[,clustering_selected]
# Correct SFARI Scores
dataset$gene.score = genes_info$gene.score
# GSEA Results
load('./../Data/GSEA_bonferroni.RData')
SFARI_colour_hue = function(r) {
pal = c('#FF7631','#FFB100','#E8E328','#8CC83F','#62CCA6','#59B9C9','#b3b3b3','#808080','gray','#d9d9d9')[r]
}
rm(DE_info, GO_annotations, clusterings, getinfo, mart, dds, GO_neuronal)
Module-Diagnosis Correlation
plot_data = dataset %>% dplyr::select(Module, MTcor) %>% distinct
ggplotly(plot_data %>% ggplot(aes(reorder(Module, -MTcor), MTcor)) + geom_bar(stat='identity', fill = plot_data$Module) + theme_minimal() +
xlab('Modules')+ ylab('Module-Diagnosis Correlation') + geom_hline(yintercept =c(0.9, -0.9), color = 'gray', linetype = 'dashed') +
theme(axis.text.x = element_text(angle = 90, hjust = 1)))
top_modules = plot_data %>% arrange(desc(MTcor)) %>% filter(abs(MTcor)>0.9) %>% dplyr::pull(Module) %>%
unique %>% as.character
cat(paste0('Top modules selected: ', paste(top_modules, collapse=', '),'\n'))
## Top modules selected: #73B000, #EE8045, #00B9E3, #84AD00
print_results = function(enrichment_list){
for(module in top_modules){
df = enrichment_list[[module]] %>% dplyr::select(ID, Description, setSize, NES, p.adjust, qvalues) %>%
arrange(desc(NES)) %>% filter(NES>0, p.adjust<0.05)
if(nrow(df)>0){
print(kable(df, caption = paste0('Enriched terms for module ', module, ' (MTcor = ',
round(dataset$MTcor[dataset$Module==module][1],2),')')))
cat('\n')
} else {
df = enrichment_list[[module]] %>% dplyr::select(ID, Description, setSize, NES, p.adjust, qvalues) %>%
arrange(desc(NES)) %>% filter(p.adjust<0.05)
if(nrow(df)>0){
print(kable(df, caption = paste0('Negatively Enriched terms for module ', module, ' (MTcor = ',
round(dataset$MTcor[dataset$Module==module][1],2),')')))
cat('\n')
} else cat(paste0('\nNo enrichment found for module ',module,'\n'))
}
}
}
GSEA Results
KEGG
print_results(enrichment_KEGG)
Enriched terms for module #73B000 (MTcor = 0.94)
| hsa05322 |
Systemic lupus erythematosus |
108 |
3.153606 |
0.0059327 |
0.0002077 |
| hsa05034 |
Alcoholism |
165 |
2.459042 |
0.0058904 |
0.0002077 |
| hsa04061 |
Viral protein interaction with cytokine and cytokine receptor |
52 |
2.281161 |
0.0060269 |
0.0002077 |
| hsa05202 |
Transcriptional misregulation in cancer |
163 |
2.203888 |
0.0059057 |
0.0002077 |
| hsa05144 |
Malaria |
39 |
2.157958 |
0.0060429 |
0.0002077 |
| hsa04392 |
Hippo signaling pathway - multiple species |
26 |
2.125743 |
0.0241726 |
0.0005221 |
| hsa05321 |
Inflammatory bowel disease (IBD) |
47 |
2.112495 |
0.0120419 |
0.0003279 |
| hsa05150 |
Staphylococcus aureus infection |
49 |
2.105556 |
0.0060243 |
0.0002077 |
| hsa04064 |
NF-kappa B signaling pathway |
89 |
2.084849 |
0.0059586 |
0.0002077 |
| hsa04060 |
Cytokine-cytokine receptor interaction |
170 |
2.038993 |
0.0058959 |
0.0002077 |
| hsa05203 |
Viral carcinogenesis |
188 |
1.947256 |
0.0058775 |
0.0002077 |
| hsa05205 |
Proteoglycans in cancer |
190 |
1.767234 |
0.0176180 |
0.0004244 |
| hsa05206 |
MicroRNAs in cancer |
155 |
1.749387 |
0.0295820 |
0.0005615 |
| hsa04510 |
Focal adhesion |
192 |
1.729820 |
0.0294080 |
0.0005615 |
| hsa05168 |
Herpes simplex virus 1 infection |
446 |
1.684611 |
0.0056711 |
0.0002077 |
| hsa05131 |
Shigellosis |
229 |
1.679445 |
0.0291453 |
0.0005615 |
Enriched terms for module #EE8045 (MTcor = 0.93)
| hsa05322 |
Systemic lupus erythematosus |
108 |
3.116966 |
0.0051117 |
0.0002189 |
| hsa05168 |
Herpes simplex virus 1 infection |
446 |
2.552720 |
0.0043657 |
0.0002189 |
| hsa05202 |
Transcriptional misregulation in cancer |
163 |
2.476862 |
0.0049160 |
0.0002189 |
| hsa05150 |
Staphylococcus aureus infection |
49 |
2.470281 |
0.0054361 |
0.0002189 |
| hsa05034 |
Alcoholism |
165 |
2.468803 |
0.0049104 |
0.0002189 |
| hsa04064 |
NF-kappa B signaling pathway |
89 |
2.297403 |
0.0052044 |
0.0002189 |
| hsa04610 |
Complement and coagulation cascades |
61 |
2.180640 |
0.0053376 |
0.0002189 |
| hsa05321 |
Inflammatory bowel disease (IBD) |
47 |
2.167627 |
0.0054505 |
0.0002189 |
| hsa04392 |
Hippo signaling pathway - multiple species |
26 |
2.114051 |
0.0394716 |
0.0007043 |
| hsa04061 |
Viral protein interaction with cytokine and cytokine receptor |
52 |
2.110892 |
0.0054038 |
0.0002189 |
| hsa05320 |
Autoimmune thyroid disease |
28 |
2.106539 |
0.0224633 |
0.0004130 |
| hsa05416 |
Viral myocarditis |
52 |
2.074541 |
0.0108075 |
0.0002249 |
| hsa05134 |
Legionellosis |
52 |
2.069673 |
0.0162113 |
0.0003073 |
| hsa05203 |
Viral carcinogenesis |
188 |
2.006682 |
0.0048435 |
0.0002189 |
| hsa04060 |
Cytokine-cytokine receptor interaction |
170 |
1.967226 |
0.0049041 |
0.0002189 |
| hsa04621 |
NOD-like receptor signaling pathway |
148 |
1.808400 |
0.0148797 |
0.0002912 |
Enriched terms for module #00B9E3 (MTcor = -0.93)
| hsa00190 |
Oxidative phosphorylation |
127 |
2.755517 |
0.0047049 |
0.0001315 |
| hsa05016 |
Huntington disease |
289 |
2.603602 |
0.0042150 |
0.0001315 |
| hsa05012 |
Parkinson disease |
235 |
2.563026 |
0.0043358 |
0.0001315 |
| hsa04723 |
Retrograde endocannabinoid signaling |
142 |
2.388517 |
0.0046292 |
0.0001315 |
| hsa04721 |
Synaptic vesicle cycle |
70 |
2.379935 |
0.0050547 |
0.0001315 |
| hsa05010 |
Alzheimer disease |
348 |
2.343123 |
0.0041027 |
0.0001315 |
| hsa04260 |
Cardiac muscle contraction |
79 |
2.298468 |
0.0049764 |
0.0001315 |
| hsa04970 |
Salivary secretion |
72 |
2.282474 |
0.0050353 |
0.0001315 |
| hsa05033 |
Nicotine addiction |
35 |
2.280163 |
0.0054286 |
0.0001315 |
| hsa04114 |
Oocyte meiosis |
108 |
2.236445 |
0.0047818 |
0.0001315 |
| hsa00020 |
Citrate cycle (TCA cycle) |
29 |
2.232058 |
0.0110237 |
0.0002169 |
| hsa04720 |
Long-term potentiation |
65 |
2.231082 |
0.0050997 |
0.0001315 |
| hsa04728 |
Dopaminergic synapse |
125 |
2.211123 |
0.0047074 |
0.0001315 |
| hsa03050 |
Proteasome |
43 |
2.188132 |
0.0053222 |
0.0001315 |
| hsa04727 |
GABAergic synapse |
82 |
2.182124 |
0.0049599 |
0.0001315 |
| hsa05017 |
Spinocerebellar ataxia |
124 |
2.165103 |
0.0047085 |
0.0001315 |
| hsa04932 |
Non-alcoholic fatty liver disease (NAFLD) |
139 |
2.162103 |
0.0046522 |
0.0001315 |
| hsa04714 |
Thermogenesis |
220 |
2.150838 |
0.0043835 |
0.0001315 |
| hsa04961 |
Endocrine and other factor-regulated calcium reabsorption |
48 |
2.137410 |
0.0052562 |
0.0001315 |
| hsa04713 |
Circadian entrainment |
93 |
2.128948 |
0.0048844 |
0.0001315 |
| hsa04724 |
Glutamatergic synapse |
108 |
2.106738 |
0.0095637 |
0.0002054 |
| hsa04740 |
Olfactory transduction |
76 |
2.058759 |
0.0050016 |
0.0001315 |
| hsa05031 |
Amphetamine addiction |
63 |
2.055094 |
0.0051199 |
0.0001315 |
| hsa05032 |
Morphine addiction |
85 |
2.045752 |
0.0049297 |
0.0001315 |
| hsa04020 |
Calcium signaling pathway |
184 |
1.969428 |
0.0044889 |
0.0001315 |
| hsa04070 |
Phosphatidylinositol signaling system |
95 |
1.955506 |
0.0048702 |
0.0001315 |
| hsa04925 |
Aldosterone synthesis and secretion |
91 |
1.940975 |
0.0097879 |
0.0002054 |
| hsa04929 |
GnRH secretion |
60 |
1.932295 |
0.0412067 |
0.0006634 |
| hsa04261 |
Adrenergic signaling in cardiomyocytes |
141 |
1.918299 |
0.0046345 |
0.0001315 |
| hsa04921 |
Oxytocin signaling pathway |
149 |
1.917718 |
0.0045945 |
0.0001315 |
| hsa04750 |
Inflammatory mediator regulation of TRP channels |
94 |
1.881673 |
0.0195223 |
0.0003414 |
| hsa04725 |
Cholinergic synapse |
106 |
1.879938 |
0.0191920 |
0.0003414 |
| hsa04910 |
Insulin signaling pathway |
130 |
1.797130 |
0.0421438 |
0.0006634 |
Enriched terms for module #84AD00 (MTcor = -0.93)
| hsa00190 |
Oxidative phosphorylation |
127 |
2.945789 |
0.0061467 |
0.0002020 |
| hsa05016 |
Huntington disease |
289 |
2.675672 |
0.0059725 |
0.0002020 |
| hsa00020 |
Citrate cycle (TCA cycle) |
29 |
2.597006 |
0.0063968 |
0.0002020 |
| hsa05012 |
Parkinson disease |
235 |
2.585831 |
0.0060325 |
0.0002020 |
| hsa04260 |
Cardiac muscle contraction |
79 |
2.332358 |
0.0062790 |
0.0002020 |
| hsa05010 |
Alzheimer disease |
348 |
2.314316 |
0.0059151 |
0.0002020 |
| hsa04721 |
Synaptic vesicle cycle |
70 |
2.294327 |
0.0062638 |
0.0002020 |
| hsa04714 |
Thermogenesis |
220 |
2.234977 |
0.0060494 |
0.0002020 |
| hsa03050 |
Proteasome |
43 |
2.233015 |
0.0063597 |
0.0002020 |
| hsa04932 |
Non-alcoholic fatty liver disease (NAFLD) |
139 |
2.173141 |
0.0061074 |
0.0002020 |
| hsa01210 |
2-Oxocarboxylic acid metabolism |
16 |
2.134622 |
0.0259289 |
0.0006706 |
| hsa01200 |
Carbon metabolism |
109 |
2.127586 |
0.0061770 |
0.0002020 |
| hsa04723 |
Retrograde endocannabinoid signaling |
142 |
2.098863 |
0.0061081 |
0.0002020 |
| hsa04728 |
Dopaminergic synapse |
125 |
2.012312 |
0.0061470 |
0.0002020 |
| hsa04961 |
Endocrine and other factor-regulated calcium reabsorption |
48 |
2.012073 |
0.0442044 |
0.0009997 |
| hsa05017 |
Spinocerebellar ataxia |
124 |
1.969167 |
0.0061532 |
0.0002020 |
| hsa01230 |
Biosynthesis of amino acids |
68 |
1.967095 |
0.0376334 |
0.0009141 |
| hsa04910 |
Insulin signaling pathway |
130 |
1.918522 |
0.0061312 |
0.0002020 |
| hsa04740 |
Olfactory transduction |
76 |
1.916677 |
0.0438764 |
0.0009997 |
| hsa04925 |
Aldosterone synthesis and secretion |
91 |
1.916531 |
0.0062171 |
0.0002020 |
| hsa04261 |
Adrenergic signaling in cardiomyocytes |
141 |
1.873656 |
0.0061158 |
0.0002020 |
| hsa04020 |
Calcium signaling pathway |
184 |
1.678485 |
0.0487277 |
0.0010653 |
|
|
|
|
|
|
Reactome
print_results(enrichment_Reactome)
Enriched terms for module #73B000 (MTcor = 0.94)
| R-HSA-5625886 |
Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 |
59 |
3.404989 |
0.0251148 |
0.0001590 |
| R-HSA-5334118 |
DNA methylation |
57 |
3.354489 |
0.0251134 |
0.0001590 |
| R-HSA-2299718 |
Condensation of Prophase Chromosomes |
66 |
3.346491 |
0.0250763 |
0.0001590 |
| R-HSA-73728 |
RNA Polymerase I Promoter Opening |
57 |
3.315263 |
0.0251134 |
0.0001590 |
| R-HSA-427359 |
SIRT1 negatively regulates rRNA expression |
62 |
3.250592 |
0.0251285 |
0.0001590 |
| R-HSA-212300 |
PRC2 methylates histones and DNA |
67 |
3.227406 |
0.0250861 |
0.0001590 |
| R-HSA-912446 |
Meiotic recombination |
77 |
3.195567 |
0.0250397 |
0.0001590 |
| R-HSA-1912408 |
Pre-NOTCH Transcription and Translation |
87 |
3.192122 |
0.0250673 |
0.0001590 |
| R-HSA-427389 |
ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression |
70 |
3.166086 |
0.0251176 |
0.0001590 |
| R-HSA-1912422 |
Pre-NOTCH Expression and Processing |
103 |
3.120790 |
0.0250294 |
0.0001590 |
| R-HSA-8936459 |
RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function |
87 |
3.120711 |
0.0250673 |
0.0001590 |
| R-HSA-5625740 |
RHO GTPases activate PKNs |
87 |
3.100816 |
0.0250673 |
0.0001590 |
| R-HSA-201722 |
Formation of the beta-catenin:TCF transactivating complex |
83 |
3.071049 |
0.0250927 |
0.0001590 |
| R-HSA-977225 |
Amyloid fiber formation |
92 |
3.054978 |
0.0249353 |
0.0001590 |
| R-HSA-171306 |
Packaging Of Telomere Ends |
45 |
3.053194 |
0.0252883 |
0.0001590 |
| R-HSA-1500620 |
Meiosis |
106 |
3.047447 |
0.0249511 |
0.0001590 |
| R-HSA-2559582 |
Senescence-Associated Secretory Phenotype (SASP) |
103 |
3.033487 |
0.0250294 |
0.0001590 |
| R-HSA-3214815 |
HDACs deacetylate histones |
89 |
3.027939 |
0.0250215 |
0.0001590 |
| R-HSA-110330 |
Recognition and association of DNA glycosylase with site containing an affected purine |
49 |
3.020401 |
0.0251918 |
0.0001590 |
| R-HSA-110331 |
Cleavage of the damaged purine |
49 |
3.020401 |
0.0251918 |
0.0001590 |
| R-HSA-73927 |
Depurination |
49 |
3.020401 |
0.0251918 |
0.0001590 |
| R-HSA-1474165 |
Reproduction |
121 |
3.018783 |
0.0249159 |
0.0001590 |
| R-HSA-5617472 |
Activation of anterior HOX genes in hindbrain development during early embryogenesis |
105 |
3.005654 |
0.0249660 |
0.0001590 |
| R-HSA-5619507 |
Activation of HOX genes during differentiation |
105 |
3.005654 |
0.0249660 |
0.0001590 |
| R-HSA-73772 |
RNA Polymerase I Promoter Escape |
85 |
2.995694 |
0.0250505 |
0.0001590 |
| R-HSA-9018519 |
Estrogen-dependent gene expression |
139 |
2.977948 |
0.0247648 |
0.0001590 |
| R-HSA-3214842 |
HDMs demethylate histones |
50 |
2.973280 |
0.0251648 |
0.0001590 |
| R-HSA-1221632 |
Meiotic synapsis |
69 |
2.972464 |
0.0251148 |
0.0001590 |
| R-HSA-5250924 |
B-WICH complex positively regulates rRNA expression |
85 |
2.968917 |
0.0250505 |
0.0001590 |
| R-HSA-5578749 |
Transcriptional regulation by small RNAs |
100 |
2.925635 |
0.0250196 |
0.0001590 |
| R-HSA-110328 |
Recognition and association of DNA glycosylase with site containing an affected pyrimidine |
54 |
2.921933 |
0.0251435 |
0.0001590 |
| R-HSA-110329 |
Cleavage of the damaged pyrimidine |
54 |
2.921933 |
0.0251435 |
0.0001590 |
| R-HSA-73928 |
Depyrimidination |
54 |
2.921933 |
0.0251435 |
0.0001590 |
| R-HSA-606279 |
Deposition of new CENPA-containing nucleosomes at the centromere |
67 |
2.897203 |
0.0250861 |
0.0001590 |
| R-HSA-774815 |
Nucleosome assembly |
67 |
2.897203 |
0.0250861 |
0.0001590 |
| R-HSA-73929 |
Base-Excision Repair, AP Site Formation |
56 |
2.892719 |
0.0251228 |
0.0001590 |
| R-HSA-3214858 |
RMTs methylate histone arginines |
74 |
2.859401 |
0.0251318 |
0.0001590 |
| R-HSA-427413 |
NoRC negatively regulates rRNA expression |
100 |
2.815700 |
0.0250196 |
0.0001590 |
| R-HSA-68875 |
Mitotic Prophase |
134 |
2.803678 |
0.0248199 |
0.0001590 |
| R-HSA-5250913 |
Positive epigenetic regulation of rRNA expression |
100 |
2.789580 |
0.0250196 |
0.0001590 |
| R-HSA-2559586 |
DNA Damage/Telomere Stress Induced Senescence |
72 |
2.789390 |
0.0251223 |
0.0001590 |
| R-HSA-5250941 |
Negative epigenetic regulation of rRNA expression |
103 |
2.768677 |
0.0250294 |
0.0001590 |
| R-HSA-73864 |
RNA Polymerase I Transcription |
105 |
2.759782 |
0.0249660 |
0.0001590 |
| R-HSA-73854 |
RNA Polymerase I Promoter Clearance |
104 |
2.732154 |
0.0250247 |
0.0001590 |
| R-HSA-3214841 |
PKMTs methylate histone lysines |
68 |
2.710487 |
0.0251059 |
0.0001590 |
| R-HSA-2559580 |
Oxidative Stress Induced Senescence |
116 |
2.699026 |
0.0249135 |
0.0001590 |
| R-HSA-157579 |
Telomere Maintenance |
74 |
2.672800 |
0.0251318 |
0.0001590 |
| R-HSA-211000 |
Gene Silencing by RNA |
128 |
2.604248 |
0.0247987 |
0.0001590 |
| R-HSA-3214847 |
HATs acetylate histones |
134 |
2.598060 |
0.0248199 |
0.0001590 |
| R-HSA-8939211 |
ESR-mediated signaling |
205 |
2.590280 |
0.0244928 |
0.0001590 |
| R-HSA-73884 |
Base Excision Repair |
84 |
2.546982 |
0.0250805 |
0.0001590 |
| R-HSA-8939236 |
RUNX1 regulates transcription of genes involved in differentiation of HSCs |
120 |
2.515455 |
0.0249302 |
0.0001590 |
| R-HSA-6785807 |
Interleukin-4 and Interleukin-13 signaling |
88 |
2.497601 |
0.0250439 |
0.0001590 |
| R-HSA-73886 |
Chromosome Maintenance |
101 |
2.483760 |
0.0249846 |
0.0001590 |
| R-HSA-2559583 |
Cellular Senescence |
183 |
2.480288 |
0.0246088 |
0.0001590 |
| R-HSA-212165 |
Epigenetic regulation of gene expression |
140 |
2.462506 |
0.0247974 |
0.0001590 |
| R-HSA-5693571 |
Nonhomologous End-Joining (NHEJ) |
66 |
2.460174 |
0.0250763 |
0.0001590 |
| R-HSA-6783783 |
Interleukin-10 signaling |
34 |
2.418768 |
0.0252845 |
0.0001590 |
| R-HSA-5693565 |
Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks |
73 |
2.396526 |
0.0251252 |
0.0001590 |
| R-HSA-5693606 |
DNA Double Strand Break Response |
74 |
2.396061 |
0.0251318 |
0.0001590 |
| R-HSA-9006931 |
Signaling by Nuclear Receptors |
244 |
2.381399 |
0.0243898 |
0.0001590 |
| R-HSA-1566948 |
Elastic fibre formation |
43 |
2.370406 |
0.0252611 |
0.0001590 |
| R-HSA-8941326 |
RUNX2 regulates bone development |
30 |
2.351001 |
0.0252954 |
0.0001590 |
| R-HSA-69473 |
G2/M DNA damage checkpoint |
91 |
2.341737 |
0.0249683 |
0.0001590 |
| R-HSA-5693607 |
Processing of DNA double-strand break ends |
94 |
2.341501 |
0.0249725 |
0.0001590 |
| R-HSA-1474244 |
Extracellular matrix organization |
263 |
2.331853 |
0.0243579 |
0.0001590 |
| R-HSA-1266695 |
Interleukin-7 signaling |
33 |
2.306149 |
0.0253327 |
0.0001590 |
| R-HSA-3247509 |
Chromatin modifying enzymes |
259 |
2.278873 |
0.0243207 |
0.0001590 |
| R-HSA-4839726 |
Chromatin organization |
259 |
2.278873 |
0.0243207 |
0.0001590 |
| R-HSA-5693567 |
HDR through Homologous Recombination (HRR) or Single Strand Annealing (SSA) |
126 |
2.235138 |
0.0248641 |
0.0001590 |
| R-HSA-157118 |
Signaling by NOTCH |
224 |
2.214671 |
0.0244334 |
0.0001590 |
| R-HSA-8878171 |
Transcriptional regulation by RUNX1 |
218 |
2.201971 |
0.0244490 |
0.0001590 |
| R-HSA-5693538 |
Homology Directed Repair |
132 |
2.171556 |
0.0248447 |
0.0001590 |
| R-HSA-3000170 |
Syndecan interactions |
27 |
2.155250 |
0.0253136 |
0.0001590 |
| R-HSA-3108232 |
SUMO E3 ligases SUMOylate target proteins |
175 |
2.093088 |
0.0245655 |
0.0001590 |
| R-HSA-1474290 |
Collagen formation |
84 |
2.086264 |
0.0250805 |
0.0001590 |
| R-HSA-201681 |
TCF dependent signaling in response to WNT |
215 |
2.034284 |
0.0244125 |
0.0001590 |
| R-HSA-2990846 |
SUMOylation |
181 |
2.007948 |
0.0245606 |
0.0001590 |
| R-HSA-5693532 |
DNA Double-Strand Break Repair |
160 |
1.923506 |
0.0246523 |
0.0001590 |
| R-HSA-195258 |
RHO GTPase Effectors |
304 |
1.840488 |
0.0241978 |
0.0001590 |
| R-HSA-449147 |
Signaling by Interleukins |
393 |
1.805721 |
0.0238851 |
0.0001590 |
| R-HSA-195721 |
Signaling by WNT |
309 |
1.690092 |
0.0484043 |
0.0002494 |
| R-HSA-68886 |
M Phase |
370 |
1.647770 |
0.0479453 |
0.0002489 |
| R-HSA-2262752 |
Cellular responses to stress |
405 |
1.632674 |
0.0477761 |
0.0002489 |
Enriched terms for module #EE8045 (MTcor = 0.93)
| R-HSA-5625886 |
Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 |
59 |
3.428710 |
0.0224452 |
0.0001374 |
| R-HSA-5334118 |
DNA methylation |
57 |
3.406522 |
0.0225278 |
0.0001374 |
| R-HSA-73728 |
RNA Polymerase I Promoter Opening |
57 |
3.355613 |
0.0225278 |
0.0001374 |
| R-HSA-2299718 |
Condensation of Prophase Chromosomes |
66 |
3.267881 |
0.0222082 |
0.0001374 |
| R-HSA-427359 |
SIRT1 negatively regulates rRNA expression |
62 |
3.259000 |
0.0223359 |
0.0001374 |
| R-HSA-212300 |
PRC2 methylates histones and DNA |
67 |
3.195257 |
0.0221954 |
0.0001374 |
| R-HSA-3214815 |
HDACs deacetylate histones |
89 |
3.183673 |
0.0217741 |
0.0001374 |
| R-HSA-912446 |
Meiotic recombination |
77 |
3.177327 |
0.0220402 |
0.0001374 |
| R-HSA-1912408 |
Pre-NOTCH Transcription and Translation |
87 |
3.167742 |
0.0218376 |
0.0001374 |
| R-HSA-427389 |
ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression |
70 |
3.166898 |
0.0221338 |
0.0001374 |
| R-HSA-8936459 |
RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function |
87 |
3.142486 |
0.0218376 |
0.0001374 |
| R-HSA-5625740 |
RHO GTPases activate PKNs |
87 |
3.092663 |
0.0218376 |
0.0001374 |
| R-HSA-1500620 |
Meiosis |
106 |
3.041621 |
0.0214335 |
0.0001374 |
| R-HSA-171306 |
Packaging Of Telomere Ends |
45 |
3.029616 |
0.0228412 |
0.0001374 |
| R-HSA-73772 |
RNA Polymerase I Promoter Escape |
85 |
3.024781 |
0.0218633 |
0.0001374 |
| R-HSA-1221632 |
Meiotic synapsis |
69 |
3.021587 |
0.0221711 |
0.0001374 |
| R-HSA-1912422 |
Pre-NOTCH Expression and Processing |
103 |
2.995518 |
0.0214362 |
0.0001374 |
| R-HSA-1474165 |
Reproduction |
121 |
2.990888 |
0.0211577 |
0.0001374 |
| R-HSA-977225 |
Amyloid fiber formation |
92 |
2.976874 |
0.0216948 |
0.0001374 |
| R-HSA-110330 |
Recognition and association of DNA glycosylase with site containing an affected purine |
49 |
2.955917 |
0.0227469 |
0.0001374 |
| R-HSA-110331 |
Cleavage of the damaged purine |
49 |
2.955917 |
0.0227469 |
0.0001374 |
| R-HSA-73927 |
Depurination |
49 |
2.955917 |
0.0227469 |
0.0001374 |
| R-HSA-5250924 |
B-WICH complex positively regulates rRNA expression |
85 |
2.945840 |
0.0218633 |
0.0001374 |
| R-HSA-201722 |
Formation of the beta-catenin:TCF transactivating complex |
83 |
2.931072 |
0.0218740 |
0.0001374 |
| R-HSA-2559582 |
Senescence-Associated Secretory Phenotype (SASP) |
103 |
2.919696 |
0.0214362 |
0.0001374 |
| R-HSA-427413 |
NoRC negatively regulates rRNA expression |
100 |
2.872722 |
0.0214971 |
0.0001374 |
| R-HSA-5617472 |
Activation of anterior HOX genes in hindbrain development during early embryogenesis |
105 |
2.867060 |
0.0214081 |
0.0001374 |
| R-HSA-5619507 |
Activation of HOX genes during differentiation |
105 |
2.867060 |
0.0214081 |
0.0001374 |
| R-HSA-5578749 |
Transcriptional regulation by small RNAs |
100 |
2.865456 |
0.0214971 |
0.0001374 |
| R-HSA-9018519 |
Estrogen-dependent gene expression |
139 |
2.861305 |
0.0208499 |
0.0001374 |
| R-HSA-110328 |
Recognition and association of DNA glycosylase with site containing an affected pyrimidine |
54 |
2.857918 |
0.0225696 |
0.0001374 |
| R-HSA-110329 |
Cleavage of the damaged pyrimidine |
54 |
2.857918 |
0.0225696 |
0.0001374 |
| R-HSA-73928 |
Depyrimidination |
54 |
2.857918 |
0.0225696 |
0.0001374 |
| R-HSA-2559586 |
DNA Damage/Telomere Stress Induced Senescence |
72 |
2.845834 |
0.0220842 |
0.0001374 |
| R-HSA-606279 |
Deposition of new CENPA-containing nucleosomes at the centromere |
67 |
2.832629 |
0.0221954 |
0.0001374 |
| R-HSA-774815 |
Nucleosome assembly |
67 |
2.832629 |
0.0221954 |
0.0001374 |
| R-HSA-73929 |
Base-Excision Repair, AP Site Formation |
56 |
2.824304 |
0.0225502 |
0.0001374 |
| R-HSA-5250941 |
Negative epigenetic regulation of rRNA expression |
103 |
2.813435 |
0.0214362 |
0.0001374 |
| R-HSA-3214842 |
HDMs demethylate histones |
50 |
2.792860 |
0.0227196 |
0.0001374 |
| R-HSA-73864 |
RNA Polymerase I Transcription |
105 |
2.772099 |
0.0214081 |
0.0001374 |
| R-HSA-73854 |
RNA Polymerase I Promoter Clearance |
104 |
2.753275 |
0.0214122 |
0.0001374 |
| R-HSA-5250913 |
Positive epigenetic regulation of rRNA expression |
100 |
2.745753 |
0.0214971 |
0.0001374 |
| R-HSA-3214858 |
RMTs methylate histone arginines |
74 |
2.745707 |
0.0220896 |
0.0001374 |
| R-HSA-3214847 |
HATs acetylate histones |
134 |
2.695651 |
0.0209365 |
0.0001374 |
| R-HSA-68875 |
Mitotic Prophase |
134 |
2.687889 |
0.0209365 |
0.0001374 |
| R-HSA-157579 |
Telomere Maintenance |
74 |
2.678335 |
0.0220896 |
0.0001374 |
| R-HSA-5693565 |
Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks |
73 |
2.669142 |
0.0220969 |
0.0001374 |
| R-HSA-5693606 |
DNA Double Strand Break Response |
74 |
2.658132 |
0.0220896 |
0.0001374 |
| R-HSA-211000 |
Gene Silencing by RNA |
128 |
2.636333 |
0.0209926 |
0.0001374 |
| R-HSA-5693571 |
Nonhomologous End-Joining (NHEJ) |
66 |
2.633793 |
0.0222082 |
0.0001374 |
| R-HSA-3214841 |
PKMTs methylate histone lysines |
68 |
2.560910 |
0.0221843 |
0.0001374 |
| R-HSA-212165 |
Epigenetic regulation of gene expression |
140 |
2.555835 |
0.0208463 |
0.0001374 |
| R-HSA-2559580 |
Oxidative Stress Induced Senescence |
116 |
2.542884 |
0.0212351 |
0.0001374 |
| R-HSA-73886 |
Chromosome Maintenance |
101 |
2.490931 |
0.0215019 |
0.0001374 |
| R-HSA-73884 |
Base Excision Repair |
84 |
2.481520 |
0.0218801 |
0.0001374 |
| R-HSA-8939236 |
RUNX1 regulates transcription of genes involved in differentiation of HSCs |
120 |
2.458849 |
0.0211600 |
0.0001374 |
| R-HSA-8939211 |
ESR-mediated signaling |
205 |
2.449368 |
0.0200212 |
0.0001374 |
| R-HSA-69473 |
G2/M DNA damage checkpoint |
91 |
2.394096 |
0.0217515 |
0.0001374 |
| R-HSA-5693607 |
Processing of DNA double-strand break ends |
94 |
2.388162 |
0.0216587 |
0.0001374 |
| R-HSA-3247509 |
Chromatin modifying enzymes |
259 |
2.382042 |
0.0195119 |
0.0001374 |
| R-HSA-4839726 |
Chromatin organization |
259 |
2.382042 |
0.0195119 |
0.0001374 |
| R-HSA-1474290 |
Collagen formation |
84 |
2.337750 |
0.0218801 |
0.0001374 |
| R-HSA-2559583 |
Cellular Senescence |
183 |
2.295883 |
0.0202788 |
0.0001374 |
| R-HSA-8878171 |
Transcriptional regulation by RUNX1 |
218 |
2.261105 |
0.0198763 |
0.0001374 |
| R-HSA-2022090 |
Assembly of collagen fibrils and other multimeric structures |
56 |
2.236997 |
0.0225502 |
0.0001374 |
| R-HSA-5693567 |
HDR through Homologous Recombination (HRR) or Single Strand Annealing (SSA) |
126 |
2.229659 |
0.0210738 |
0.0001374 |
| R-HSA-6785807 |
Interleukin-4 and Interleukin-13 signaling |
88 |
2.229070 |
0.0218120 |
0.0001374 |
| R-HSA-9006931 |
Signaling by Nuclear Receptors |
244 |
2.206897 |
0.0196781 |
0.0001374 |
| R-HSA-1474244 |
Extracellular matrix organization |
263 |
2.206092 |
0.0194762 |
0.0001374 |
| R-HSA-1650814 |
Collagen biosynthesis and modifying enzymes |
65 |
2.192422 |
0.0222185 |
0.0001374 |
| R-HSA-5693538 |
Homology Directed Repair |
132 |
2.149519 |
0.0210048 |
0.0001374 |
| R-HSA-216083 |
Integrin cell surface interactions |
75 |
2.089222 |
0.0220449 |
0.0001374 |
| R-HSA-3108232 |
SUMO E3 ligases SUMOylate target proteins |
175 |
2.071740 |
0.0203379 |
0.0001374 |
| R-HSA-4551638 |
SUMOylation of chromatin organization proteins |
70 |
2.046488 |
0.0442675 |
0.0001501 |
| R-HSA-5693532 |
DNA Double-Strand Break Repair |
160 |
2.018206 |
0.0205764 |
0.0001374 |
| R-HSA-2990846 |
SUMOylation |
181 |
1.979695 |
0.0202852 |
0.0001374 |
| R-HSA-157118 |
Signaling by NOTCH |
224 |
1.951114 |
0.0198181 |
0.0001374 |
| R-HSA-1474228 |
Degradation of the extracellular matrix |
117 |
1.880459 |
0.0424171 |
0.0001454 |
| R-HSA-195258 |
RHO GTPase Effectors |
304 |
1.829443 |
0.0191205 |
0.0001374 |
| R-HSA-194315 |
Signaling by Rho GTPases |
427 |
1.815317 |
0.0183115 |
0.0001374 |
| R-HSA-201681 |
TCF dependent signaling in response to WNT |
215 |
1.685616 |
0.0398614 |
0.0001399 |
| R-HSA-449147 |
Signaling by Interleukins |
393 |
1.646806 |
0.0185323 |
0.0001374 |
| R-HSA-68886 |
M Phase |
370 |
1.603246 |
0.0186825 |
0.0001374 |
Enriched terms for module #00B9E3 (MTcor = -0.93)
| R-HSA-163200 |
Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. |
122 |
2.771562 |
0.0197786 |
0.0003057 |
| R-HSA-1428517 |
The citric acid (TCA) cycle and respiratory electron transport |
170 |
2.722842 |
0.0189276 |
0.0003057 |
| R-HSA-611105 |
Respiratory electron transport |
100 |
2.712848 |
0.0202396 |
0.0003057 |
| R-HSA-112316 |
Neuronal System |
379 |
2.643595 |
0.0169280 |
0.0003057 |
| R-HSA-112315 |
Transmission across Chemical Synapses |
245 |
2.572379 |
0.0179982 |
0.0003057 |
| R-HSA-180024 |
DARPP-32 events |
25 |
2.566180 |
0.0231774 |
0.0003057 |
| R-HSA-5576892 |
Phase 0 - rapid depolarisation |
45 |
2.542660 |
0.0219888 |
0.0003057 |
| R-HSA-1296072 |
Voltage gated Potassium channels |
40 |
2.533345 |
0.0222219 |
0.0003057 |
| R-HSA-399719 |
Trafficking of AMPA receptors |
30 |
2.525597 |
0.0228369 |
0.0003057 |
| R-HSA-399721 |
Glutamate binding, activation of AMPA receptors and synaptic plasticity |
30 |
2.525597 |
0.0228369 |
0.0003057 |
| R-HSA-112314 |
Neurotransmitter receptors and postsynaptic signal transmission |
184 |
2.501833 |
0.0187214 |
0.0003057 |
| R-HSA-6799198 |
Complex I biogenesis |
55 |
2.486575 |
0.0215979 |
0.0003057 |
| R-HSA-442755 |
Activation of NMDA receptors and postsynaptic events |
84 |
2.413330 |
0.0206268 |
0.0003057 |
| R-HSA-438066 |
Unblocking of NMDA receptors, glutamate binding and activation |
22 |
2.398864 |
0.0233726 |
0.0003057 |
| R-HSA-445095 |
Interaction between L1 and Ankyrins |
29 |
2.389660 |
0.0228525 |
0.0003057 |
| R-HSA-442982 |
Ras activation upon Ca2+ influx through NMDA receptor |
21 |
2.358380 |
0.0234935 |
0.0003057 |
| R-HSA-9620244 |
Long-term potentiation |
24 |
2.331833 |
0.0231806 |
0.0003057 |
| R-HSA-9617324 |
Negative regulation of NMDA receptor-mediated neuronal transmission |
22 |
2.316670 |
0.0233726 |
0.0003057 |
| R-HSA-438064 |
Post NMDA receptor activation events |
73 |
2.314038 |
0.0210213 |
0.0003057 |
| R-HSA-5682910 |
LGI-ADAM interactions |
14 |
2.302572 |
0.0241829 |
0.0003057 |
| R-HSA-416993 |
Trafficking of GluR2-containing AMPA receptors |
16 |
2.294111 |
0.0239491 |
0.0003057 |
| R-HSA-6794362 |
Protein-protein interactions at synapses |
87 |
2.281273 |
0.0205509 |
0.0003057 |
| R-HSA-1489509 |
DAG and IP3 signaling |
41 |
2.253555 |
0.0221843 |
0.0003057 |
| R-HSA-111933 |
Calmodulin induced events |
35 |
2.244918 |
0.0224995 |
0.0003057 |
| R-HSA-111997 |
CaM pathway |
35 |
2.244918 |
0.0224995 |
0.0003057 |
| R-HSA-8849932 |
Synaptic adhesion-like molecules |
21 |
2.236925 |
0.0469870 |
0.0004354 |
| R-HSA-1296071 |
Potassium Channels |
92 |
2.209534 |
0.0204446 |
0.0003057 |
| R-HSA-168799 |
Neurotoxicity of clostridium toxins |
10 |
2.193865 |
0.0494018 |
0.0004437 |
| R-HSA-442742 |
CREB1 phosphorylation through NMDA receptor-mediated activation of RAS signaling |
29 |
2.190215 |
0.0228525 |
0.0003057 |
| R-HSA-5576891 |
Cardiac conduction |
131 |
2.186421 |
0.0196061 |
0.0003057 |
| R-HSA-5339562 |
Uptake and actions of bacterial toxins |
30 |
2.186355 |
0.0228369 |
0.0003057 |
| R-HSA-111885 |
Opioid Signalling |
86 |
2.173169 |
0.0205528 |
0.0003057 |
| R-HSA-111996 |
Ca-dependent events |
37 |
2.168548 |
0.0447450 |
0.0004302 |
| R-HSA-1168372 |
Downstream signaling events of B Cell Receptor (BCR) |
81 |
2.166032 |
0.0207344 |
0.0003057 |
| R-HSA-888590 |
GABA synthesis, release, reuptake and degradation |
19 |
2.161818 |
0.0472005 |
0.0004354 |
| R-HSA-442720 |
CREB1 phosphorylation through the activation of Adenylate Cyclase |
13 |
2.151123 |
0.0484717 |
0.0004412 |
| R-HSA-1236978 |
Cross-presentation of soluble exogenous antigens (endosomes) |
47 |
2.149661 |
0.0219284 |
0.0003057 |
| R-HSA-210500 |
Glutamate Neurotransmitter Release Cycle |
24 |
2.146751 |
0.0463612 |
0.0004354 |
| R-HSA-69052 |
Switching of origins to a post-replicative state |
87 |
2.142347 |
0.0205509 |
0.0003057 |
| R-HSA-5578775 |
Ion homeostasis |
53 |
2.140474 |
0.0216580 |
0.0003057 |
| R-HSA-68827 |
CDT1 association with the CDC6:ORC:origin complex |
57 |
2.130876 |
0.0215175 |
0.0003057 |
| R-HSA-68867 |
Assembly of the pre-replicative complex |
65 |
2.128218 |
0.0212570 |
0.0003057 |
| R-HSA-5610783 |
Degradation of GLI2 by the proteasome |
57 |
2.115002 |
0.0215175 |
0.0003057 |
| R-HSA-112310 |
Neurotransmitter release cycle |
47 |
2.106833 |
0.0219284 |
0.0003057 |
| R-HSA-8986944 |
Transcriptional Regulation by MECP2 |
61 |
2.090800 |
0.0213952 |
0.0003057 |
| R-HSA-5610785 |
GLI3 is processed to GLI3R by the proteasome |
57 |
2.082944 |
0.0215175 |
0.0003057 |
| R-HSA-2454202 |
Fc epsilon receptor (FCERI) signaling |
129 |
2.079485 |
0.0196412 |
0.0003057 |
| R-HSA-68949 |
Orc1 removal from chromatin |
69 |
2.077892 |
0.0210941 |
0.0003057 |
| R-HSA-5610780 |
Degradation of GLI1 by the proteasome |
57 |
2.075156 |
0.0215175 |
0.0003057 |
| R-HSA-5676590 |
NIK–>noncanonical NF-kB signaling |
56 |
2.066272 |
0.0215590 |
0.0003057 |
| R-HSA-174113 |
SCF-beta-TrCP mediated degradation of Emi1 |
53 |
2.034135 |
0.0216580 |
0.0003057 |
| R-HSA-8939902 |
Regulation of RUNX2 expression and activity |
70 |
2.018323 |
0.0421516 |
0.0004217 |
| R-HSA-174084 |
Autodegradation of Cdh1 by Cdh1:APC/C |
62 |
2.018057 |
0.0427044 |
0.0004217 |
| R-HSA-176408 |
Regulation of APC/C activators between G1/S and early anaphase |
76 |
2.013606 |
0.0418253 |
0.0004217 |
| R-HSA-6794361 |
Neurexins and neuroligins |
56 |
2.008824 |
0.0431180 |
0.0004217 |
| R-HSA-5607761 |
Dectin-1 mediated noncanonical NF-kB signaling |
57 |
2.008410 |
0.0430349 |
0.0004217 |
| R-HSA-5610787 |
Hedgehog ‘off’ state |
108 |
2.001968 |
0.0200302 |
0.0003057 |
| R-HSA-9604323 |
Negative regulation of NOTCH4 signaling |
54 |
1.999309 |
0.0432453 |
0.0004217 |
| R-HSA-983705 |
Signaling by the B Cell Receptor (BCR) |
107 |
1.998265 |
0.0200599 |
0.0003057 |
| R-HSA-69017 |
CDK-mediated phosphorylation and removal of Cdc6 |
69 |
1.989499 |
0.0421881 |
0.0004217 |
| R-HSA-373760 |
L1CAM interactions |
111 |
1.940906 |
0.0399737 |
0.0004217 |
| R-HSA-5607764 |
CLEC7A (Dectin-1) signaling |
98 |
1.921267 |
0.0406331 |
0.0004217 |
| R-HSA-983168 |
Antigen processing: Ubiquitination & Proteasome degradation |
296 |
1.889138 |
0.0175230 |
0.0003057 |
| R-HSA-5673001 |
RAF/MAP kinase cascade |
224 |
1.863297 |
0.0181937 |
0.0003057 |
| R-HSA-397014 |
Muscle contraction |
187 |
1.841178 |
0.0187025 |
0.0003057 |
| R-HSA-5684996 |
MAPK1/MAPK3 signaling |
230 |
1.806671 |
0.0181680 |
0.0003057 |
| R-HSA-8951664 |
Neddylation |
225 |
1.772501 |
0.0363849 |
0.0004217 |
| R-HSA-5683057 |
MAPK family signaling cascades |
266 |
1.739480 |
0.0177747 |
0.0003057 |
| R-HSA-1852241 |
Organelle biogenesis and maintenance |
286 |
1.730102 |
0.0176001 |
0.0003057 |
| R-HSA-69620 |
Cell Cycle Checkpoints |
279 |
1.688245 |
0.0176632 |
0.0003057 |
Enriched terms for module #84AD00 (MTcor = -0.93)
| R-HSA-1428517 |
The citric acid (TCA) cycle and respiratory electron transport |
170 |
3.030448 |
0.0256882 |
0.0002955 |
| R-HSA-611105 |
Respiratory electron transport |
100 |
2.953639 |
0.0261010 |
0.0002955 |
| R-HSA-163200 |
Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. |
122 |
2.931129 |
0.0258897 |
0.0002955 |
| R-HSA-5576892 |
Phase 0 - rapid depolarisation |
45 |
2.640552 |
0.0265488 |
0.0002955 |
| R-HSA-6799198 |
Complex I biogenesis |
55 |
2.632292 |
0.0265415 |
0.0002955 |
| R-HSA-888590 |
GABA synthesis, release, reuptake and degradation |
19 |
2.531137 |
0.0269022 |
0.0002955 |
| R-HSA-71406 |
Pyruvate metabolism and Citric Acid (TCA) cycle |
52 |
2.519440 |
0.0265678 |
0.0002955 |
| R-HSA-71403 |
Citric acid cycle (TCA cycle) |
22 |
2.480228 |
0.0268220 |
0.0002955 |
| R-HSA-112316 |
Neuronal System |
379 |
2.473304 |
0.0247369 |
0.0002955 |
| R-HSA-1296072 |
Voltage gated Potassium channels |
40 |
2.452507 |
0.0265594 |
0.0002955 |
| R-HSA-399719 |
Trafficking of AMPA receptors |
30 |
2.429160 |
0.0266492 |
0.0002955 |
| R-HSA-399721 |
Glutamate binding, activation of AMPA receptors and synaptic plasticity |
30 |
2.429160 |
0.0266492 |
0.0002955 |
| R-HSA-1268020 |
Mitochondrial protein import |
63 |
2.427393 |
0.0263920 |
0.0002955 |
| R-HSA-5682910 |
LGI-ADAM interactions |
14 |
2.425477 |
0.0269563 |
0.0002955 |
| R-HSA-112315 |
Transmission across Chemical Synapses |
245 |
2.416597 |
0.0253870 |
0.0002955 |
| R-HSA-180024 |
DARPP-32 events |
25 |
2.406851 |
0.0267465 |
0.0002955 |
| R-HSA-442982 |
Ras activation upon Ca2+ influx through NMDA receptor |
21 |
2.375977 |
0.0268801 |
0.0002955 |
| R-HSA-5339562 |
Uptake and actions of bacterial toxins |
30 |
2.311167 |
0.0266492 |
0.0002955 |
| R-HSA-112310 |
Neurotransmitter release cycle |
47 |
2.301053 |
0.0265631 |
0.0002955 |
| R-HSA-442755 |
Activation of NMDA receptors and postsynaptic events |
84 |
2.242816 |
0.0262123 |
0.0002955 |
| R-HSA-5389840 |
Mitochondrial translation elongation |
86 |
2.235272 |
0.0262236 |
0.0002955 |
| R-HSA-112314 |
Neurotransmitter receptors and postsynaptic signal transmission |
184 |
2.229291 |
0.0255794 |
0.0002955 |
| R-HSA-111933 |
Calmodulin induced events |
35 |
2.223602 |
0.0266275 |
0.0002955 |
| R-HSA-111997 |
CaM pathway |
35 |
2.223602 |
0.0266275 |
0.0002955 |
| R-HSA-5368287 |
Mitochondrial translation |
92 |
2.210952 |
0.0261086 |
0.0002955 |
| R-HSA-5368286 |
Mitochondrial translation initiation |
86 |
2.170356 |
0.0262236 |
0.0002955 |
| R-HSA-5419276 |
Mitochondrial translation termination |
86 |
2.166536 |
0.0262236 |
0.0002955 |
| R-HSA-351202 |
Metabolism of polyamines |
83 |
2.144309 |
0.0261657 |
0.0002955 |
| R-HSA-111885 |
Opioid Signalling |
86 |
2.136095 |
0.0262236 |
0.0002955 |
| R-HSA-438064 |
Post NMDA receptor activation events |
73 |
2.114563 |
0.0262900 |
0.0002955 |
| R-HSA-1296071 |
Potassium Channels |
92 |
2.093680 |
0.0261086 |
0.0002955 |
| R-HSA-9609507 |
Protein localization |
158 |
2.020541 |
0.0258224 |
0.0002955 |
| R-HSA-5628897 |
TP53 Regulates Metabolic Genes |
84 |
1.970919 |
0.0262123 |
0.0002955 |
| R-HSA-8951664 |
Neddylation |
225 |
1.969353 |
0.0254564 |
0.0002955 |
| R-HSA-5576891 |
Cardiac conduction |
131 |
1.937803 |
0.0258647 |
0.0002955 |
| R-HSA-163685 |
Integration of energy metabolism |
101 |
1.905819 |
0.0260721 |
0.0002955 |
| R-HSA-8856688 |
Golgi-to-ER retrograde transport |
124 |
1.869820 |
0.0258747 |
0.0002955 |
| R-HSA-5610787 |
Hedgehog ‘off’ state |
108 |
1.864307 |
0.0259791 |
0.0002955 |
| R-HSA-1852241 |
Organelle biogenesis and maintenance |
286 |
1.728487 |
0.0252216 |
0.0002955 |
|
|
|
|
|
|
Gene Ontology
print_results(enrichment_GO)
No enrichment found for module #73B000
No enrichment found for module #EE8045
No enrichment found for module #00B9E3
No enrichment found for module #84AD00
Disease Ontology
print_results(enrichment_DO)
Enriched terms for module #73B000 (MTcor = 0.94)
| DOID:1936 |
atherosclerosis |
280 |
2.328354 |
0.0141355 |
0.0000646 |
| DOID:1115 |
sarcoma |
173 |
2.326923 |
0.0143437 |
0.0000646 |
| DOID:2348 |
arteriosclerotic cardiovascular disease |
281 |
2.319477 |
0.0141406 |
0.0000646 |
| DOID:2349 |
arteriosclerosis |
287 |
2.304857 |
0.0141348 |
0.0000646 |
| DOID:2213 |
hemorrhagic disease |
121 |
2.270698 |
0.0145040 |
0.0000646 |
| DOID:0050161 |
lower respiratory tract disease |
391 |
2.258512 |
0.0139636 |
0.0000646 |
| DOID:552 |
pneumonia |
78 |
2.257550 |
0.0146515 |
0.0000646 |
| DOID:3770 |
pulmonary fibrosis |
101 |
2.254562 |
0.0145592 |
0.0000646 |
| DOID:1579 |
respiratory system disease |
429 |
2.239237 |
0.0138906 |
0.0000646 |
| DOID:850 |
lung disease |
383 |
2.238401 |
0.0139628 |
0.0000646 |
| DOID:3083 |
chronic obstructive pulmonary disease |
174 |
2.222449 |
0.0143482 |
0.0000646 |
| DOID:3717 |
gastric adenocarcinoma |
81 |
2.214898 |
0.0146567 |
0.0000646 |
| DOID:2218 |
blood platelet disease |
76 |
2.212813 |
0.0146649 |
0.0000646 |
| DOID:5520 |
head and neck squamous cell carcinoma |
153 |
2.211620 |
0.0143988 |
0.0000646 |
| DOID:3082 |
interstitial lung disease |
136 |
2.199707 |
0.0145166 |
0.0000646 |
| DOID:2320 |
obstructive lung disease |
229 |
2.198971 |
0.0142248 |
0.0000646 |
| DOID:7148 |
rheumatoid arthritis |
430 |
2.196661 |
0.0138820 |
0.0000646 |
| DOID:10534 |
stomach cancer |
231 |
2.187767 |
0.0142008 |
0.0000646 |
| DOID:13133 |
HELLP syndrome |
15 |
2.169495 |
0.0300954 |
0.0001198 |
| DOID:4330 |
non-langerhans-cell histiocytosis |
11 |
2.167417 |
0.0300395 |
0.0001198 |
| DOID:520 |
aortic disease |
48 |
2.155743 |
0.0295192 |
0.0001198 |
| DOID:1247 |
blood coagulation disease |
142 |
2.155103 |
0.0144770 |
0.0000646 |
| DOID:11934 |
head and neck cancer |
209 |
2.151208 |
0.0142719 |
0.0000646 |
| DOID:104 |
bacterial infectious disease |
191 |
2.144434 |
0.0143042 |
0.0000646 |
| DOID:14504 |
Niemann-Pick disease |
10 |
2.141539 |
0.0300544 |
0.0001198 |
| DOID:3627 |
aortic aneurysm |
47 |
2.130650 |
0.0443138 |
0.0001681 |
| DOID:1542 |
head and neck carcinoma |
206 |
2.128565 |
0.0143157 |
0.0000646 |
| DOID:37 |
skin disease |
254 |
2.125717 |
0.0141908 |
0.0000646 |
| DOID:1793 |
pancreatic cancer |
276 |
2.111636 |
0.0141465 |
0.0000646 |
| DOID:1588 |
thrombocytopenia |
57 |
2.110410 |
0.0294471 |
0.0001198 |
| DOID:4362 |
cervical cancer |
96 |
2.106032 |
0.0145975 |
0.0000646 |
| DOID:1520 |
colon carcinoma |
149 |
2.105316 |
0.0144346 |
0.0000646 |
| DOID:409 |
liver disease |
500 |
2.104661 |
0.0137786 |
0.0000646 |
| DOID:5517 |
stomach carcinoma |
133 |
2.103167 |
0.0145019 |
0.0000646 |
| DOID:201 |
connective tissue cancer |
338 |
2.099796 |
0.0140341 |
0.0000646 |
| DOID:4905 |
pancreatic carcinoma |
206 |
2.098585 |
0.0143157 |
0.0000646 |
| DOID:4481 |
allergic rhinitis |
67 |
2.096063 |
0.0146891 |
0.0000646 |
| DOID:1176 |
bronchial disease |
104 |
2.091506 |
0.0145449 |
0.0000646 |
| DOID:824 |
periodontitis |
88 |
2.090860 |
0.0146400 |
0.0000646 |
| DOID:3326 |
purpura |
57 |
2.087347 |
0.0294471 |
0.0001198 |
| DOID:2893 |
cervix carcinoma |
95 |
2.083596 |
0.0145964 |
0.0000646 |
| DOID:2163 |
nasal cavity disease |
69 |
2.078487 |
0.0147015 |
0.0000646 |
| DOID:2825 |
nose disease |
69 |
2.078487 |
0.0147015 |
0.0000646 |
| DOID:4483 |
rhinitis |
69 |
2.078487 |
0.0147015 |
0.0000646 |
| DOID:3388 |
periodontal disease |
99 |
2.072415 |
0.0145655 |
0.0000646 |
| DOID:0050338 |
primary bacterial infectious disease |
165 |
2.071690 |
0.0144081 |
0.0000646 |
| DOID:170 |
endocrine gland cancer |
443 |
2.066980 |
0.0138445 |
0.0000646 |
| DOID:854 |
collagen disease |
159 |
2.056954 |
0.0144179 |
0.0000646 |
| DOID:10124 |
corneal disease |
46 |
2.055284 |
0.0443707 |
0.0001681 |
| DOID:2151 |
malignant ovarian surface epithelial-stromal neoplasm |
256 |
2.041443 |
0.0142160 |
0.0000646 |
| DOID:2152 |
ovary epithelial cancer |
256 |
2.041443 |
0.0142160 |
0.0000646 |
| DOID:4001 |
ovarian carcinoma |
256 |
2.041443 |
0.0142160 |
0.0000646 |
| DOID:0060100 |
musculoskeletal system cancer |
395 |
2.035164 |
0.0139410 |
0.0000646 |
| DOID:219 |
colon cancer |
252 |
2.034711 |
0.0142155 |
0.0000646 |
| DOID:0060058 |
lymphoma |
66 |
2.031428 |
0.0146775 |
0.0000646 |
| DOID:9256 |
colorectal cancer |
256 |
2.031151 |
0.0142160 |
0.0000646 |
| DOID:3310 |
atopic dermatitis |
92 |
2.031063 |
0.0145779 |
0.0000646 |
| DOID:120 |
female reproductive organ cancer |
393 |
2.029211 |
0.0139514 |
0.0000646 |
| DOID:5672 |
large intestine cancer |
257 |
2.029211 |
0.0141949 |
0.0000646 |
| DOID:4960 |
bone marrow cancer |
274 |
2.021302 |
0.0141557 |
0.0000646 |
| DOID:9538 |
multiple myeloma |
221 |
2.020293 |
0.0142745 |
0.0000646 |
| DOID:16 |
integumentary system disease |
288 |
2.020174 |
0.0141139 |
0.0000646 |
| DOID:6713 |
cerebrovascular disease |
98 |
2.015214 |
0.0145836 |
0.0000646 |
| DOID:1091 |
tooth disease |
114 |
2.013934 |
0.0145609 |
0.0000646 |
| DOID:2237 |
hepatitis |
345 |
2.011724 |
0.0140208 |
0.0000646 |
| DOID:0070004 |
myeloma |
269 |
2.010450 |
0.0141805 |
0.0000646 |
| DOID:399 |
tuberculosis |
106 |
2.009155 |
0.0145344 |
0.0000646 |
| DOID:3910 |
lung adenocarcinoma |
153 |
1.998887 |
0.0143988 |
0.0000646 |
| DOID:2394 |
ovarian cancer |
276 |
1.993121 |
0.0141465 |
0.0000646 |
| DOID:2916 |
hypersensitivity reaction type IV disease |
70 |
1.987438 |
0.0440994 |
0.0001681 |
| DOID:1612 |
breast cancer |
451 |
1.987036 |
0.0138379 |
0.0000646 |
| DOID:5093 |
thoracic cancer |
451 |
1.987036 |
0.0138379 |
0.0000646 |
| DOID:1575 |
rheumatic disease |
147 |
1.985583 |
0.0144391 |
0.0000646 |
| DOID:418 |
systemic scleroderma |
147 |
1.985583 |
0.0144391 |
0.0000646 |
| DOID:419 |
scleroderma |
147 |
1.985583 |
0.0144391 |
0.0000646 |
| DOID:10155 |
intestinal cancer |
268 |
1.978959 |
0.0141867 |
0.0000646 |
| DOID:5082 |
liver cirrhosis |
173 |
1.977049 |
0.0143437 |
0.0000646 |
| DOID:3908 |
non-small cell lung carcinoma |
370 |
1.971734 |
0.0139860 |
0.0000646 |
| DOID:3905 |
lung carcinoma |
441 |
1.967848 |
0.0138396 |
0.0000646 |
| DOID:11054 |
urinary bladder cancer |
90 |
1.964252 |
0.0146427 |
0.0000646 |
| DOID:10283 |
prostate cancer |
364 |
1.960564 |
0.0140005 |
0.0000646 |
| DOID:2043 |
hepatitis B |
160 |
1.945112 |
0.0144059 |
0.0000646 |
| DOID:4074 |
pancreas adenocarcinoma |
142 |
1.942827 |
0.0144770 |
0.0000646 |
| DOID:1040 |
chronic lymphocytic leukemia |
167 |
1.934531 |
0.0143951 |
0.0000646 |
| DOID:2723 |
dermatitis |
123 |
1.928381 |
0.0145148 |
0.0000646 |
| DOID:974 |
upper respiratory tract disease |
86 |
1.928198 |
0.0437573 |
0.0001681 |
| DOID:5041 |
esophageal cancer |
127 |
1.904152 |
0.0145341 |
0.0000646 |
| DOID:8398 |
osteoarthritis |
158 |
1.902832 |
0.0144264 |
0.0000646 |
| DOID:8692 |
myeloid leukemia |
124 |
1.902192 |
0.0145242 |
0.0000646 |
| DOID:2841 |
asthma |
91 |
1.898807 |
0.0292472 |
0.0001198 |
| DOID:10952 |
nephritis |
118 |
1.888222 |
0.0290483 |
0.0001198 |
| DOID:417 |
hypersensitivity reaction type II disease |
444 |
1.887243 |
0.0138447 |
0.0000646 |
| DOID:403 |
mouth disease |
136 |
1.887171 |
0.0290333 |
0.0001198 |
| DOID:3856 |
male reproductive organ cancer |
372 |
1.886447 |
0.0139778 |
0.0000646 |
| DOID:184 |
bone cancer |
224 |
1.885886 |
0.0142564 |
0.0000646 |
| DOID:3393 |
coronary artery disease |
268 |
1.885598 |
0.0141867 |
0.0000646 |
| DOID:3347 |
osteosarcoma |
204 |
1.880283 |
0.0142974 |
0.0000646 |
| DOID:688 |
embryonal cancer |
316 |
1.871146 |
0.0140769 |
0.0000646 |
| DOID:114 |
heart disease |
420 |
1.870466 |
0.0138783 |
0.0000646 |
| DOID:5844 |
myocardial infarction |
220 |
1.868891 |
0.0142691 |
0.0000646 |
| DOID:3459 |
breast carcinoma |
339 |
1.854647 |
0.0140220 |
0.0000646 |
| DOID:4451 |
renal carcinoma |
328 |
1.853181 |
0.0140582 |
0.0000646 |
| DOID:1883 |
hepatitis C |
190 |
1.846083 |
0.0143147 |
0.0000646 |
| DOID:4195 |
hyperglycemia |
110 |
1.840590 |
0.0436801 |
0.0001681 |
| DOID:2994 |
germ cell cancer |
343 |
1.836173 |
0.0140100 |
0.0000646 |
| DOID:3996 |
urinary system cancer |
426 |
1.831902 |
0.0138683 |
0.0000646 |
| DOID:9352 |
type 2 diabetes mellitus |
166 |
1.831581 |
0.0288363 |
0.0001198 |
| DOID:1492 |
eye and adnexa disease |
441 |
1.829360 |
0.0138396 |
0.0000646 |
| DOID:4766 |
embryoma |
298 |
1.828122 |
0.0141147 |
0.0000646 |
| DOID:5614 |
eye disease |
432 |
1.813335 |
0.0138781 |
0.0000646 |
| DOID:0050155 |
sensory system disease |
489 |
1.786407 |
0.0138079 |
0.0000646 |
| DOID:557 |
kidney disease |
374 |
1.766649 |
0.0139798 |
0.0000646 |
| DOID:0060072 |
benign neoplasm |
474 |
1.760866 |
0.0138142 |
0.0000646 |
| DOID:263 |
kidney cancer |
375 |
1.760670 |
0.0139738 |
0.0000646 |
| DOID:4450 |
renal cell carcinoma |
294 |
1.752802 |
0.0141368 |
0.0000646 |
| DOID:1037 |
lymphoblastic leukemia |
359 |
1.746446 |
0.0140083 |
0.0000646 |
| DOID:18 |
urinary system disease |
387 |
1.742797 |
0.0139544 |
0.0000646 |
| DOID:0060084 |
cell type benign neoplasm |
396 |
1.717393 |
0.0139259 |
0.0000646 |
| DOID:74 |
hematopoietic system disease |
366 |
1.664221 |
0.0140083 |
0.0000646 |
| DOID:657 |
adenoma |
278 |
1.656929 |
0.0424373 |
0.0001676 |
| DOID:0050736 |
autosomal dominant disease |
360 |
1.620271 |
0.0140068 |
0.0000646 |
| DOID:3093 |
nervous system cancer |
499 |
1.618691 |
0.0137836 |
0.0000646 |
| DOID:10763 |
hypertension |
482 |
1.580088 |
0.0275518 |
0.0001198 |
Enriched terms for module #EE8045 (MTcor = 0.93)
| DOID:7148 |
rheumatoid arthritis |
430 |
2.406930 |
0.0106781 |
0.0000717 |
| DOID:3083 |
chronic obstructive pulmonary disease |
174 |
2.354784 |
0.0119021 |
0.0000717 |
| DOID:2213 |
hemorrhagic disease |
121 |
2.315706 |
0.0123496 |
0.0000717 |
| DOID:1588 |
thrombocytopenia |
57 |
2.284217 |
0.0130870 |
0.0000717 |
| DOID:3770 |
pulmonary fibrosis |
101 |
2.278557 |
0.0125472 |
0.0000717 |
| DOID:0050161 |
lower respiratory tract disease |
391 |
2.276961 |
0.0108113 |
0.0000717 |
| DOID:1579 |
respiratory system disease |
429 |
2.273814 |
0.0106829 |
0.0000717 |
| DOID:2320 |
obstructive lung disease |
229 |
2.272892 |
0.0115597 |
0.0000717 |
| DOID:850 |
lung disease |
383 |
2.266257 |
0.0108398 |
0.0000717 |
| DOID:1247 |
blood coagulation disease |
142 |
2.265142 |
0.0121645 |
0.0000717 |
| DOID:9446 |
cholangitis |
25 |
2.255001 |
0.0138001 |
0.0000749 |
| DOID:3388 |
periodontal disease |
99 |
2.231499 |
0.0125639 |
0.0000717 |
| DOID:3082 |
interstitial lung disease |
136 |
2.231101 |
0.0122120 |
0.0000717 |
| DOID:0060049 |
autoimmune disease of urogenital tract |
56 |
2.217154 |
0.0130863 |
0.0000717 |
| DOID:12236 |
primary biliary cirrhosis |
56 |
2.217154 |
0.0130863 |
0.0000717 |
| DOID:9074 |
systemic lupus erythematosus |
58 |
2.217005 |
0.0130850 |
0.0000717 |
| DOID:1115 |
sarcoma |
173 |
2.209575 |
0.0118957 |
0.0000717 |
| DOID:3326 |
purpura |
57 |
2.205286 |
0.0261739 |
0.0001338 |
| DOID:2218 |
blood platelet disease |
76 |
2.203795 |
0.0128457 |
0.0000717 |
| DOID:4481 |
allergic rhinitis |
67 |
2.201114 |
0.0129694 |
0.0000717 |
| DOID:1040 |
chronic lymphocytic leukemia |
167 |
2.196968 |
0.0119612 |
0.0000717 |
| DOID:2163 |
nasal cavity disease |
69 |
2.192375 |
0.0129535 |
0.0000717 |
| DOID:2825 |
nose disease |
69 |
2.192375 |
0.0129535 |
0.0000717 |
| DOID:4483 |
rhinitis |
69 |
2.192375 |
0.0129535 |
0.0000717 |
| DOID:824 |
periodontitis |
88 |
2.192074 |
0.0126812 |
0.0000717 |
| DOID:2916 |
hypersensitivity reaction type IV disease |
70 |
2.178799 |
0.0129258 |
0.0000717 |
| DOID:8857 |
lupus erythematosus |
62 |
2.165345 |
0.0130310 |
0.0000717 |
| DOID:974 |
upper respiratory tract disease |
86 |
2.150957 |
0.0127097 |
0.0000717 |
| DOID:1091 |
tooth disease |
114 |
2.150849 |
0.0124174 |
0.0000717 |
| DOID:11335 |
sarcoidosis |
66 |
2.149124 |
0.0259538 |
0.0001338 |
| DOID:8398 |
osteoarthritis |
158 |
2.148051 |
0.0120238 |
0.0000717 |
| DOID:1176 |
bronchial disease |
104 |
2.147108 |
0.0124946 |
0.0000717 |
| DOID:1936 |
atherosclerosis |
280 |
2.132366 |
0.0112663 |
0.0000717 |
| DOID:2348 |
arteriosclerotic cardiovascular disease |
281 |
2.129309 |
0.0112619 |
0.0000717 |
| DOID:2473 |
opportunistic mycosis |
27 |
2.125544 |
0.0411613 |
0.0001937 |
| DOID:10952 |
nephritis |
118 |
2.119637 |
0.0123714 |
0.0000717 |
| DOID:2349 |
arteriosclerosis |
287 |
2.118736 |
0.0112205 |
0.0000717 |
| DOID:552 |
pneumonia |
78 |
2.099390 |
0.0128142 |
0.0000717 |
| DOID:2841 |
asthma |
91 |
2.077346 |
0.0126525 |
0.0000717 |
| DOID:8692 |
myeloid leukemia |
124 |
2.072009 |
0.0123179 |
0.0000717 |
| DOID:612 |
primary immunodeficiency disease |
158 |
2.064591 |
0.0120238 |
0.0000717 |
| DOID:11934 |
head and neck cancer |
209 |
2.061705 |
0.0116792 |
0.0000717 |
| DOID:1542 |
head and neck carcinoma |
206 |
2.054663 |
0.0116903 |
0.0000717 |
| DOID:0060058 |
lymphoma |
66 |
2.051627 |
0.0389307 |
0.0001848 |
| DOID:399 |
tuberculosis |
106 |
2.049425 |
0.0125026 |
0.0000717 |
| DOID:9538 |
multiple myeloma |
221 |
2.039118 |
0.0116078 |
0.0000717 |
| DOID:9741 |
biliary tract disease |
71 |
2.036162 |
0.0387428 |
0.0001848 |
| DOID:104 |
bacterial infectious disease |
191 |
2.030575 |
0.0117797 |
0.0000717 |
| DOID:12361 |
Graves’ disease |
63 |
2.028658 |
0.0260517 |
0.0001338 |
| DOID:5082 |
liver cirrhosis |
173 |
2.025518 |
0.0118957 |
0.0000717 |
| DOID:5520 |
head and neck squamous cell carcinoma |
153 |
2.018823 |
0.0120762 |
0.0000717 |
| DOID:11054 |
urinary bladder cancer |
90 |
2.014636 |
0.0126652 |
0.0000717 |
| DOID:4138 |
bile duct disease |
70 |
2.007146 |
0.0387773 |
0.0001848 |
| DOID:37 |
skin disease |
254 |
1.996581 |
0.0114104 |
0.0000717 |
| DOID:417 |
hypersensitivity reaction type II disease |
444 |
1.993203 |
0.0106488 |
0.0000717 |
| DOID:4960 |
bone marrow cancer |
274 |
1.990757 |
0.0112936 |
0.0000717 |
| DOID:0070004 |
myeloma |
269 |
1.988499 |
0.0113169 |
0.0000717 |
| DOID:403 |
mouth disease |
136 |
1.988237 |
0.0122120 |
0.0000717 |
| DOID:1037 |
lymphoblastic leukemia |
359 |
1.980895 |
0.0109087 |
0.0000717 |
| DOID:10534 |
stomach cancer |
231 |
1.962774 |
0.0115542 |
0.0000717 |
| DOID:16 |
integumentary system disease |
288 |
1.961439 |
0.0112197 |
0.0000717 |
| DOID:854 |
collagen disease |
159 |
1.951838 |
0.0120116 |
0.0000717 |
| DOID:0050338 |
primary bacterial infectious disease |
165 |
1.946575 |
0.0119726 |
0.0000717 |
| DOID:2723 |
dermatitis |
123 |
1.942831 |
0.0123286 |
0.0000717 |
| DOID:9119 |
acute myeloid leukemia |
93 |
1.940028 |
0.0378464 |
0.0001846 |
| DOID:201 |
connective tissue cancer |
338 |
1.931140 |
0.0109980 |
0.0000717 |
| DOID:1575 |
rheumatic disease |
147 |
1.923856 |
0.0121345 |
0.0000717 |
| DOID:418 |
systemic scleroderma |
147 |
1.923856 |
0.0121345 |
0.0000717 |
| DOID:419 |
scleroderma |
147 |
1.923856 |
0.0121345 |
0.0000717 |
| DOID:5041 |
esophageal cancer |
127 |
1.918541 |
0.0123009 |
0.0000717 |
| DOID:3393 |
coronary artery disease |
268 |
1.902290 |
0.0113295 |
0.0000717 |
| DOID:1520 |
colon carcinoma |
149 |
1.890664 |
0.0121177 |
0.0000717 |
| DOID:409 |
liver disease |
500 |
1.888508 |
0.0104810 |
0.0000717 |
| DOID:526 |
Human immunodeficiency virus infectious disease |
132 |
1.886409 |
0.0122519 |
0.0000717 |
| DOID:170 |
endocrine gland cancer |
443 |
1.883490 |
0.0106500 |
0.0000717 |
| DOID:5844 |
myocardial infarction |
220 |
1.873768 |
0.0116060 |
0.0000717 |
| DOID:10283 |
prostate cancer |
364 |
1.863541 |
0.0109001 |
0.0000717 |
| DOID:1793 |
pancreatic cancer |
276 |
1.859825 |
0.0112846 |
0.0000717 |
| DOID:74 |
hematopoietic system disease |
366 |
1.854196 |
0.0108872 |
0.0000717 |
| DOID:0060100 |
musculoskeletal system cancer |
395 |
1.852221 |
0.0107932 |
0.0000717 |
| DOID:10591 |
pre-eclampsia |
217 |
1.845411 |
0.0116364 |
0.0000717 |
| DOID:5517 |
stomach carcinoma |
133 |
1.835183 |
0.0488892 |
0.0002260 |
| DOID:5683 |
hereditary breast ovarian cancer |
200 |
1.828842 |
0.0117111 |
0.0000717 |
| DOID:688 |
embryonal cancer |
316 |
1.821178 |
0.0111069 |
0.0000717 |
| DOID:3213 |
demyelinating disease |
144 |
1.820715 |
0.0364894 |
0.0001803 |
| DOID:2377 |
multiple sclerosis |
138 |
1.819929 |
0.0366201 |
0.0001803 |
| DOID:9352 |
type 2 diabetes mellitus |
166 |
1.819645 |
0.0239338 |
0.0001260 |
| DOID:2237 |
hepatitis |
345 |
1.817577 |
0.0109721 |
0.0000717 |
| DOID:3856 |
male reproductive organ cancer |
372 |
1.814937 |
0.0108669 |
0.0000717 |
| DOID:219 |
colon cancer |
252 |
1.812164 |
0.0114349 |
0.0000717 |
| DOID:2994 |
germ cell cancer |
343 |
1.803332 |
0.0109889 |
0.0000717 |
| DOID:4766 |
embryoma |
298 |
1.801106 |
0.0111856 |
0.0000717 |
| DOID:9256 |
colorectal cancer |
256 |
1.800043 |
0.0113965 |
0.0000717 |
| DOID:5672 |
large intestine cancer |
257 |
1.790947 |
0.0113963 |
0.0000717 |
| DOID:3996 |
urinary system cancer |
426 |
1.790153 |
0.0106907 |
0.0000717 |
| DOID:18 |
urinary system disease |
387 |
1.788396 |
0.0108226 |
0.0000717 |
| DOID:557 |
kidney disease |
374 |
1.782717 |
0.0108602 |
0.0000717 |
| DOID:4451 |
renal carcinoma |
328 |
1.781683 |
0.0110522 |
0.0000717 |
| DOID:3905 |
lung carcinoma |
441 |
1.762810 |
0.0106577 |
0.0000717 |
| DOID:114 |
heart disease |
420 |
1.752559 |
0.0107121 |
0.0000717 |
| DOID:4905 |
pancreatic carcinoma |
206 |
1.751490 |
0.0233807 |
0.0001243 |
| DOID:1492 |
eye and adnexa disease |
441 |
1.748146 |
0.0106577 |
0.0000717 |
| DOID:10155 |
intestinal cancer |
268 |
1.747589 |
0.0113295 |
0.0000717 |
| DOID:263 |
kidney cancer |
375 |
1.745672 |
0.0108610 |
0.0000717 |
| DOID:3908 |
non-small cell lung carcinoma |
370 |
1.729466 |
0.0108690 |
0.0000717 |
| DOID:120 |
female reproductive organ cancer |
393 |
1.729094 |
0.0107987 |
0.0000717 |
| DOID:184 |
bone cancer |
224 |
1.727615 |
0.0231596 |
0.0001243 |
| DOID:0050155 |
sensory system disease |
489 |
1.726523 |
0.0105067 |
0.0000717 |
| DOID:5614 |
eye disease |
432 |
1.720764 |
0.0106620 |
0.0000717 |
| DOID:1612 |
breast cancer |
451 |
1.703644 |
0.0106239 |
0.0000717 |
| DOID:5093 |
thoracic cancer |
451 |
1.703644 |
0.0106239 |
0.0000717 |
| DOID:15 |
reproductive system disease |
281 |
1.677028 |
0.0337858 |
0.0001695 |
| DOID:0050736 |
autosomal dominant disease |
360 |
1.669221 |
0.0109122 |
0.0000717 |
| DOID:10763 |
hypertension |
482 |
1.559100 |
0.0316265 |
0.0001601 |
Enriched terms for module #00B9E3 (MTcor = -0.93)
| DOID:2234 |
focal epilepsy |
57 |
2.205412 |
0.0252781 |
0.000262 |
| DOID:1826 |
epilepsy syndrome |
191 |
2.070965 |
0.0109172 |
0.000262 |
| DOID:0060041 |
autism spectrum disorder |
166 |
1.800904 |
0.0334385 |
0.000262 |
| DOID:12849 |
autistic disorder |
166 |
1.800904 |
0.0334385 |
0.000262 |
| DOID:0060040 |
pervasive developmental disorder |
175 |
1.780626 |
0.0332072 |
0.000262 |
Enriched terms for module #84AD00 (MTcor = -0.93)
| DOID:1826 |
epilepsy syndrome |
191 |
2.01758 |
0.0148789 |
0.000146 |
Disease Gene Network
print_results(enrichment_DGN)
No enrichment found for module #73B000
Enriched terms for module #EE8045 (MTcor = 0.93)
| umls:C3495559 |
Juvenile arthritis |
272 |
2.374540 |
0.0496448 |
0.0003302 |
| umls:C3714514 |
Infection |
464 |
2.191351 |
0.0464164 |
0.0003302 |
| umls:C0036421 |
Systemic Scleroderma |
441 |
2.101877 |
0.0466225 |
0.0003302 |
| umls:C1800706 |
Idiopathic Pulmonary Fibrosis |
276 |
2.063431 |
0.0495485 |
0.0003302 |
| umls:C0032285 |
Pneumonia |
312 |
2.046221 |
0.0488940 |
0.0003302 |
| umls:C0009319 |
Colitis |
414 |
2.016902 |
0.0470188 |
0.0003302 |
| umls:C0024115 |
Lung diseases |
276 |
1.993770 |
0.0495485 |
0.0003302 |
| umls:C0019829 |
Hodgkin Disease |
306 |
1.986978 |
0.0490109 |
0.0003302 |
| umls:C0032914 |
Pre-Eclampsia |
275 |
1.982788 |
0.0495356 |
0.0003302 |
| umls:C0024305 |
Lymphoma, Non-Hodgkin |
426 |
1.923352 |
0.0469401 |
0.0003302 |
| umls:C0003864 |
Arthritis |
427 |
1.920451 |
0.0469112 |
0.0003302 |
| umls:C0042373 |
Vascular Diseases |
328 |
1.913508 |
0.0485818 |
0.0003302 |
| umls:C0034069 |
Pulmonary Fibrosis |
290 |
1.904986 |
0.0492768 |
0.0003302 |
| umls:C0011615 |
Dermatitis, Atopic |
333 |
1.867993 |
0.0485165 |
0.0003302 |
| umls:C0014072 |
Experimental Autoimmune Encephalomyelitis |
305 |
1.864136 |
0.0490439 |
0.0003302 |
| umls:C0007570 |
Celiac Disease |
268 |
1.856958 |
0.0497089 |
0.0003302 |
| umls:C0376545 |
Hematologic Neoplasms |
399 |
1.845926 |
0.0472276 |
0.0003302 |
| umls:C0153676 |
Secondary malignant neoplasm of lung |
490 |
1.843747 |
0.0461331 |
0.0003302 |
| umls:C3272363 |
Ischemic Cerebrovascular Accident |
271 |
1.820657 |
0.0496462 |
0.0003302 |
| umls:C0023267 |
Fibroid Tumor |
270 |
1.814286 |
0.0496866 |
0.0003302 |
| umls:C0037274 |
Dermatologic disorders |
363 |
1.807124 |
0.0478928 |
0.0003302 |
| umls:C0948008 |
Ischemic stroke |
307 |
1.799159 |
0.0489780 |
0.0003302 |
| umls:C0023895 |
Liver diseases |
446 |
1.793146 |
0.0465705 |
0.0003302 |
| umls:C0021051 |
Immunologic Deficiency Syndromes |
349 |
1.789369 |
0.0481426 |
0.0003302 |
| umls:C0035126 |
Reperfusion Injury |
271 |
1.770544 |
0.0496462 |
0.0003302 |
| umls:C0278996 |
Cancer of Head and Neck |
361 |
1.768079 |
0.0479485 |
0.0003302 |
| umls:C0079744 |
Diffuse Large B-Cell Lymphoma |
459 |
1.755678 |
0.0464889 |
0.0003302 |
| umls:C1292769 |
Precursor B-cell lymphoblastic leukemia |
297 |
1.753167 |
0.0491671 |
0.0003302 |
| umls:C0013595 |
Eczema |
281 |
1.746958 |
0.0494791 |
0.0003302 |
| umls:C1519670 |
Tumor Angiogenesis |
360 |
1.746787 |
0.0479512 |
0.0003302 |
| umls:C0853879 |
Invasive breast carcinoma |
321 |
1.746492 |
0.0486779 |
0.0003302 |
| umls:C0023470 |
Myeloid Leukemia |
430 |
1.742136 |
0.0468560 |
0.0003302 |
| umls:C0409974 |
Lupus Erythematosus |
284 |
1.737924 |
0.0494440 |
0.0003302 |
| umls:C1621958 |
Glioblastoma Multiforme |
370 |
1.737153 |
0.0478239 |
0.0003302 |
| umls:C1378703 |
Renal carcinoma |
387 |
1.726801 |
0.0475113 |
0.0003302 |
| umls:C0029456 |
Osteoporosis |
368 |
1.710440 |
0.0478854 |
0.0003302 |
| umls:C0220641 |
Lip and Oral Cavity Carcinoma |
344 |
1.705676 |
0.0482859 |
0.0003302 |
| umls:C0278883 |
Metastatic melanoma |
272 |
1.704536 |
0.0496448 |
0.0003302 |
| umls:C0153381 |
Malignant neoplasm of mouth |
344 |
1.703523 |
0.0482859 |
0.0003302 |
| umls:C0023493 |
Adult T-Cell Lymphoma/Leukemia |
366 |
1.691341 |
0.0478854 |
0.0003302 |
| umls:C0085110 |
Severe Combined Immunodeficiency |
420 |
1.683272 |
0.0469652 |
0.0003302 |
| umls:C0239946 |
Fibrosis, Liver |
271 |
1.672850 |
0.0496462 |
0.0003302 |
| umls:C0019348 |
Herpes Simplex Infections |
425 |
1.620043 |
0.0469427 |
0.0003302 |
| umls:C0345904 |
Malignant neoplasm of liver |
481 |
1.618418 |
0.0461630 |
0.0003302 |
| umls:C0025286 |
Meningioma |
381 |
1.609239 |
0.0476085 |
0.0003302 |
| umls:C0152018 |
Esophageal carcinoma |
445 |
1.602814 |
0.0465977 |
0.0003302 |
| umls:C0008626 |
Congenital chromosomal disease |
440 |
1.601495 |
0.0466313 |
0.0003302 |
| umls:C0546837 |
Malignant neoplasm of esophagus |
485 |
1.593860 |
0.0461717 |
0.0003302 |
| umls:C0022661 |
Kidney Failure, Chronic |
483 |
1.589512 |
0.0461954 |
0.0003302 |
Enriched terms for module #00B9E3 (MTcor = -0.93)
| umls:C0004134 |
Ataxia |
221 |
1.957340 |
0.0467638 |
0.0015602 |
| umls:C0014556 |
Epilepsy, Temporal Lobe |
175 |
1.878511 |
0.0482947 |
0.0015602 |
| umls:C0525045 |
Mood Disorders |
238 |
1.864062 |
0.0462184 |
0.0015602 |
| umls:C1510586 |
Autism Spectrum Disorders |
216 |
1.835349 |
0.0469588 |
0.0015602 |
| umls:C1263846 |
Attention deficit hyperactivity disorder |
365 |
1.706949 |
0.0435070 |
0.0015602 |
| umls:C0004936 |
Mental disorders |
384 |
1.688912 |
0.0431365 |
0.0015602 |
No enrichment found for module #84AD00